Measuring inbreeding and inbreeding depression on pig growth from pedigree or <scp>SNP</scp>‐derived metrics

Silió, L.; Rodríguez, M. C.; Barragán, C.; Benítez, Rita; Óvilo, Cristina; Fernández, Ana

doi:10.1111/jbg.12031

Cited by 99 publications

(90 citation statements)

References 28 publications

(77 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The distribution of S ROH within breed was assessed using box plots. In addition, chromosomal (BTA) F ROH (F ROHBTA ) values were also estimated for each breed, as F ROHBTA = L ROHBTA /L BTA (Silió et al, 2013), in which L ROHBTA is the total length of an individual's ROH in each BTA and L BTA is the length of each chromosome covered by the involved SNPs (Supplementary Table S1). ROH were classified into three classes (4 to 8, 8 to 16 and >16 Mb) using the same nomenclature reported by other authors (Ferenčaković et al, 2013a;Marras et al, 2014) except for two classes (<2 and 2 to 4 Mb), which were not considered in our study.…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, estimate of F using ROH is particularly appealing as the number of generations of inbreeding and the history of recent selection events can be inferred from the extend and frequency of ROH regions (Purfield et al, 2012). Although ROH from high-throughput genotyping analyses have been studied extensively in humans, these estimates are rare in cattle, particular in local breeds, and in other livestock species (Purfield et al, 2012;Ferenčaković et al, 2013a;Silió et al, 2013;Pertoldi et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

130

124

View full text Add to dashboard Cite

In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient ( F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH ( F ROH ) in three local dairy cattle breeds. F ROH values were compared with F estimated from the genomic relationship matrix ( F GRM ), based on the difference between observed v. expected number of homozygous genotypes ( F HOM ) and the genomic homozygosity of individual i ( F MOL i ). The molecular coancestry coefficient ( f MOL ij ) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of F ROH , whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between F HOM and F ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F ROH and other estimated F coefficients were generally lower ranged from 0.45 ( F MOL i − F ROH ) in Cinisara to 0.17 ( F GRM − F ROH ) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.Keywords: genomic inbreeding, local cattle breeds, runs of homozygosity ImplicationsIn the local breeds with small population size, one of the most important problems is the increase of inbreeding that leads to different negative effects as a reduction in phenotypic values. The current study aims to quantify the genomic inbreeding derived from runs of homozygosity (ROH) (F ROH ) in three Italian local dairy cattle breeds. According to ROH results, recent inbreeding was well detected in the investigated local dairy cattle breeds. Our results showed the necessity of implementing co...

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

130

124

View full text Add to dashboard Cite

show abstract

“…While ROH from high-throughput genotyping analyses have been studied extensively in humans, such analyses are rare in cattle and other livestock species [6-10]. The lack of standards for ROH definition and identification may introduce bias in ROH-based estimates of autozygosity.…”

Section: Introductionmentioning

confidence: 99%

Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors

2013

View full text Add to dashboard Cite

BackgroundRuns of homozygosity are long, uninterrupted stretches of homozygous genotypes that enable reliable estimation of levels of inbreeding (i.e., autozygosity) based on high-throughput, chip-based single nucleotide polymorphism (SNP) genotypes. While the theoretical definition of runs of homozygosity is straightforward, their empirical identification depends on the type of SNP chip used to obtain the data and on a number of factors, including the number of heterozygous calls allowed to account for genotyping errors. We analyzed how SNP chip density and genotyping errors affect estimates of autozygosity based on runs of homozygosity in three cattle populations, using genotype data from an SNP chip with 777 972 SNPs and a 50 k chip.ResultsData from the 50 k chip led to overestimation of the number of runs of homozygosity that are shorter than 4 Mb, since the analysis could not identify heterozygous SNPs that were present on the denser chip. Conversely, data from the denser chip led to underestimation of the number of runs of homozygosity that were longer than 8 Mb, unless the presence of a small number of heterozygous SNP genotypes was allowed within a run of homozygosity.ConclusionsWe have shown that SNP chip density and genotyping errors introduce patterns of bias in the estimation of autozygosity based on runs of homozygosity. SNP chips with 50 000 to 60 000 markers are frequently available for livestock species and their information leads to a conservative prediction of autozygosity from runs of homozygosity longer than 4 Mb. Not allowing heterozygous SNP genotypes to be present in a homozygosity run, as has been advocated for human populations, is not adequate for livestock populations because they have much higher levels of autozygosity and therefore longer runs of homozygosity. When allowing a small number of heterozygous calls, current software does not differentiate between situations where these calls are adjacent and therefore indicative of an actual break of the run versus those where they are scattered across the length of the homozygous segment. Simple graphical tests that are used in this paper are a current, yet tedious solution.

show abstract

“…In livestock species, genomic estimates of inbreeding have been obtained for different cattle [8, 21, 22, 23, 24], sheep [25] and pig [26, 27] breeds, but estimates of genomic coancestry are rare [28]. However, both inbreeding and coancestry are of fundamental importance in animal breeding programmes.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

Rodríguez‐Ramilo¹,

Fernández²,

Toro

et al. 2015

PLoS ONE

View full text Add to dashboard Cite

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

show abstract

Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP‐derived metrics

Cited by 99 publications

References 28 publications

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors

Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

Contact Info

Product

Resources

About